Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach (Q42582317)

3 November 2017

Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach (English)

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3 November 2017

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Julio A Freyre-González

object named as

Julio A Freyre-González

1

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Julio Collado-Vides

object named as

Julio Collado-Vides

4

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author name string

José A Alonso-Pavón

2

1 reference

3 November 2017

Luis G Treviño-Quintanilla

3

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3 November 2017

27 October 2008

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3 November 2017

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3 November 2017

9

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3 November 2017

10

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3 November 2017

R154

1 reference

describes a project that uses

3 November 2017

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

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Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli

28 May 2018

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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).

28 May 2018

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Genomic analysis of the hierarchical structure of regulatory networks

28 May 2018

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Feed-forward loop circuits as a side effect of genome evolution

28 May 2018

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Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

28 May 2018

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Network motifs: structure does not determine function

28 May 2018

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Phenotypic variation in bacteria: the role of feedback regulation

28 May 2018

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RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

28 May 2018

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Binding and transcriptional activation of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2.

28 May 2018

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Stochasticity in gene expression: from theories to phenotypes

28 May 2018

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An evolutionary and functional assessment of regulatory network motifs

28 May 2018

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DNA supercoiling - a global transcriptional regulator for enterobacterial growth?

28 May 2018

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Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli

28 May 2018

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EcoCyc: a comprehensive database resource for Escherichia coli

28 May 2018

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An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs

28 May 2018

1 reference

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Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach

28 May 2018

1 reference

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The topological relationship between the large-scale attributes and local interaction patterns of complex networks

28 May 2018

1 reference

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The regulation of bacterial transcription initiation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

28 May 2018

1 reference

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Network biology: understanding the cell's functional organization

28 May 2018

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GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins

28 May 2018

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

28 May 2018

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Identifying global regulators in transcriptional regulatory networks in bacteria

28 May 2018

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Genetic regulatory mechanisms in the synthesis of proteins

28 May 2018

2 references

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28 May 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior

16 August 2018

1 reference

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Hierarchical organization in complex networks

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Evolution of transcription factors and the gene regulatory network in Escherichia coli

28 May 2018

1 reference

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Network motifs: simple building blocks of complex networks

28 May 2018

1 reference

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Hierarchical organization of modularity in metabolic networks

28 May 2018

1 reference

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Specificity and stability in topology of protein networks

28 May 2018

1 reference

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Network motifs in the transcriptional regulation network of Escherichia coli

28 May 2018

1 reference

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Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli

28 May 2018

1 reference

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FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions

28 May 2018

1 reference

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Error and attack tolerance of complex networks

28 May 2018

1 reference

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From molecular to modular cell biology

28 May 2018

1 reference

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Laws for the dynamics of regulatory networks.

28 May 2018

1 reference

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Coordinated repression in vitro of the divergent fepA-fes promoters of Escherichia coli by the iron uptake regulation (Fur) protein.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

The regulation of transcription initiation by integration host factor

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Bacterial regulation: global regulatory networks

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Transition of Escherichia coli from aerobic to micro-aerobic conditions involves fast and slow reacting regulatory components.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

In vitro reconstitution of catabolite repression in Escherichia coli.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Modular analysis of the transcriptional regulatory network of E. coli.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Networks, dynamics, and modularity

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Two different modes of transcription repression of the Escherichia coli acetate operon by IclR.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Evidence for "pre-recruitment" as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

The modularity of biological regulatory networks.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760881

Are network motifs the spandrels of cellular complexity?

16 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18954463

12 December 2020

inferred from PubMed ID database lookup

Iron regulates transcription of the Escherichia coli ferric citrate transport genes directly and through the transcription initiation proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18954463

12 December 2020

inferred from PubMed ID database lookup

Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18954463

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/GB-2008-9-10-R154

1 reference

Dimensions Publication ID

3 November 2017

1 reference

0 references

1 reference

3 November 2017

PubMed publication ID

18954463

1 reference